BMRB: 11347

Solution structure of the PHD domain in PHD finger protein 21A

Authors

He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

Assembly

PHD finger protein 21A

Entity

1. PHD domain (polymer, Thiol state: all other bound), 56 monomers, 6191.086 Da Detail

GSSGSSGHED FCSVCRKSGQ LLMCDTCSRV YHLDCLDPPL KTIPKGMWIC PRCQDQ

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

6321.904 Da

Max. entity weight

6191.086 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS12:SG	2:ZN1:ZN
2	na	sing	1:CYS15:SG	2:ZN1:ZN
3	na	sing	1:CYS24:SG	2:ZN1:ZN
4	na	sing	1:CYS27:SG	2:ZN1:ZN
5	na	sing	1:HIS32:ND1	2:ZN1:ZN
6	na	sing	1:CYS35:SG	2:ZN1:ZN
7	na	sing	1:CYS50:SG	2:ZN1:ZN
8	na	sing	1:CYS53:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.1 %, Completeness: 92.9 %, Completeness (bb): 89.9 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	92.9 % (577 of 621)	92.9 % (303 of 326)	93.7 % (224 of 239)	89.3 % (50 of 56)
Backbone	89.9 % (295 of 328)	88.5 % (100 of 113)	91.4 % (149 of 163)	88.5 % (46 of 52)
Sidechain	95.9 % (330 of 344)	95.3 % (203 of 213)	96.9 % (123 of 127)	100.0 % (4 of 4)
Aromatic	94.7 % (36 of 38)	94.7 % (18 of 19)	94.4 % (17 of 18)	100.0 % (1 of 1)
Methyl	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)

1. PHD domain

GSSGSSGHED FCSVCRKSGQ LLMCDTCSRV YHLDCLDPPL KTIPKGMWIC PRCQDQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.05), Details 1.0mM 13C, 15N-labeled {protein;} 20mM d-Tris-HCl(pH {7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PHD domain	[U-13C; U-15N]	protein	1.0 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	H2O		solvent	90 %
7	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.62 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.62 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.59 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 2YQL, Strand ID: A Detail

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Release date

2011-09-06

Citation

Solution structure of the PHD domain in PHD finger protein 21A
He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

Related entities 1. PHD domain, : 1 : 3 : 221 entities Detail

Interaction partners 1. PHD domain, : 35 interactors Detail

Experiments performed 2 experiments Detail